Renting a car and driving from Cologne to Mainz: Is this a one way rental that is being dropped off in Mainz? Why the stops in Bonn and Koblenz? I can see stopping at your other stops, but Bonn and Koblenz don't have the same small Rhine wine town appeal. It may take you longer to drive down than you think, as that is the tail end of European vacation season, and I'm assuming you'd be driving on the B9, which can be slow driving through all those pretty wine towns which are usually full of tourists. Have you looked at doing the train on this section as well?
Have you timed the Munich trip to avoid Oktoberfest? If not, you may have some hotel surprise.
Personally, I'd give Cologne more time than Düsseldorf if you are into cathedrals and unique architecture.